Publication highlights

Researchers at the Crick and AlveoliX have developed the first human 'lung-on-chip' model using stem cells taken from only one person. The team produced type I and II alveolar epithelial cells and vascular endothelial cells from human-induced pluripotent stem cells. These epithelial and endothelial cells are separatley grown on the top and bottom of a very thin membrane in a device to recreate an air sac barrier, which experience rhythmic three-dimensional stretching forces on the recreated air sac barrier, mimicking the motion of breathing. The scientists then added macrophages into the chip, before adding TB bacteria. In the chips infected with TB, the team reported large macrophage clusters containing a group of dead macrophages in a necrotic core.

Growth is a key feature of development, but animals, organs and tissues must know when to stop growing. Researchers at the Crick have shown that the sac-like structures that give rise to fly wings do not stop growing abruptly. Instead, growth slows down over the course of days. Measurements of global gene activity during growth deceleration suggest that, as the primordium expands, it becomes increasingly hypoxic. Decreasing oxygen availability, perhaps due to inefficient import as tissue size increases, was confirmed with new genetic sensors of cellular oxygen. This study uncovers a feedback loop whereby growth (and increasing tissue size) leads to hypoxia, which in turn dampens growth to ensure that oxygen demand does not overwhelm dwindling supplies.

Researchers at the Crick have produced a new embryo model that self-organises around ten somites alongside a single neural tube, mirroring aspects of human embryos at 28 to 35 days after fertilisation. As the models don't contain a notochord, the team introduced signals that would have originally come from a notochord, and observed a shift in cell fates. They also saw spontaneous patterning in the neurla tube, showing it was developing into different identieis depending on the cell's location. This suggested that the somites and the neural tube were in close communication. The team confirmed that increased retinoic acid signalling in specific somite regions was likely due to signalling to the neural tube, allowing spontaneous patterning. This crosstalk helps prompt regional identities and may be important for later maturation to neuronal or skeletal tissues.

Children born with mutations in the ARPC5 protein, which is part of the internal cytoskeleton, experience immunodeficiency and a high risk of sepsis. Researchers at the Crick investigated immune system function in mice with and without ARPC5 mutations, observing inflammation in adult mice with ARPC5 deficiency that mirrored that in humans. They showed that this was due to a big change in bacterial composition in the gut after weaning, triggering intestinal inflammation, as giving antibiotics to ARPC5-deficient mice at a critical four-week time point fully prevented the disease from developing. Finally, the team showed that macrophages with ARPC5 mutations had lost their usual shape and could no longer kill bacteria effectively, leading to an overwhelming response to the microbiome.

Researchers at the Crick have found that hunger can make virgin female mice aggressive towards pups, but only in certain hormonal states. These mice would usually ignore other females' pups or show parent-like caring behaviour. The team found that AgRP neurons mediated the effect of food deprivation on behaviour towards pups, by targeting the medial preoptic area. Mice at certain stages of the reproductive estrous cycle were more likely to become aggressive towards pups, dictated by the ratio of oestradiol and progesterone setting the responsiveness of MPOA neurons. They showed that hunger information carried by the AgRP neurons dampens neuronal activity in the MPOA, stimulating the switch from caring behaviour to pup-directed aggression. 

The amount of any given protein in a cell has to be controlled to keep its levels within a range required for healthy functions, which is especially important for proteins that group together in condensates which generally contain flexible parts and can form many interactions at the same time. Aiming to discover how the cell regulates the amounts of these proteins, researchers at the Crick and King's College London's UK Dementia Research Institute investigated nuclear speckles, condensates in the nucleus, discovering a new way for cells to maintain the equilibrium of many proteins that condense together. They termed this 'interstasis': how the accumulation of various proteins in a condensate can decrease further production of the same proteins by capturing their own mRNAs (messenger molecules) into the same condensate. In this way the cell can regulate genes that are particularly dose-dependent and proteins which are involved in many diseases of ageing.

About half of glioblastomas have rogue rings of DNA floating outside of chromosomes called extrachromosomal DNA (ecDNA). The Cancer Grand Challenges eDyNAmiC team, including researchers from Stanford University, Queen Mary University of London and the Crick, integrated genomic and imaging data from people with glioblastomas with advanced computational modelling of the evolution of ecDNAs in space and time. Their analysis revealed that most ecDNA rings contained EGFR, a potent cancer-driving gene. EGFR DNA appeared early in the cancer's evolution and also frequently gained extra changes that made the cancer more aggressive. The time between the first appearance of EGFR ecDNA and the emergence of more aggressive variants may represent a window of opportunity to detect and treat the disease.

Lymph nodes are small organs distributed throughout the body that orchestrate immune processes. In response to infection, vaccination, or cancer, a germinal centre (GC) forms within them, driving the maturation of memory B cells and plasma cells. Because of their 3D structure and diverse cell types, GCs are ideal for 3D imaging. This protocol describes rapid, high-resolution multicolour imaging of whole immunised lymph nodes, covering harvesting, fixation, permeabilisation, staining, and clearing. Imaging is performed with a fluorescence lightsheet microscope, and analysis with Imaris. It quantifies GC B cells, plasma cells, and follicular T cells, and includes optimised stainings for visualising other lymph node structures.

Researchers at the Crick have discovered that the heart's own contractions trigger biological signals that guide the formation of a functional beating heart. Their study in zebrafish highlights the heart's ability to remodel and adapt to physiological demands and could also reveal what goes wrong during congenital heart conditions. They followed the early development of the heart's muscular structures, called trabeculae, in zebrafish using live 4D imaging. The team observed that trabeculae don't grow and develop by cell division, as previously thought. Instead, neighbouring cells are recruited to build trabecular complexity, thus increasing the heart's muscle mass and contractile efficiency. Finally, they uncovered a feedback mechanisms between heart contraction and its own development, dictating a healthy pace of growth.

Researchers have mapped the human metabolic pathways that Cryptosporidium, an intestinal parasite, requires to survive. They conducted a genome-scale screening experiment that involves systematically disabling nearly every protein-coding gene, individually, from human intestinal cells, before infecting the cells with Cryptosporidium. The team found that genes involved in making cholesterol appeared to have opposing effects - some boosting infection and others blocking it. This balance hinged on a molecule midway through the cholesterol production line, squalene. This molecule protects against oxidative stress by stimulating the production of glutathione, which Cryptosporidium needs but cannot make. This leaves the parasite dependent on glutathione from the host cell, a dependency which can be targeted with a high cholesterol drug called lapaquistat. This drug reduced infection in a mouse model of disease and completely blocked intestinal damage, suggesting it could be repurposed to fight Cryptosporidium.

The DNA replication checkpoint is essential for maintaining genome stability. Without it, when DNA copying restarts after a stall, too many replication origins—the starting points for copying—are mistakenly activated, ultimately leading to cell death. Researchers at the Crick showed, in human cells lacking this checkpoint, that excessive DNA synthesis from surplus origins consumes the vital replication proteins PCNA and RFC, preventing normal restart of stalled copying at replication forks. Without the protection of PCNA and RFC, the ends of the forks are attacked by a protein called HLTF, causing irreversible damage. Removing HLTF helps cells survive even in the absence of the checkpoint, which has implications for how resistance to anti-checkpoint cancer therapies may arise.